I don't know if this is directly related to the transparent flagging window issue, but this seems to be a bit different. The window will only show up entirely by hovering the mouse over the area not covered by the new answer box. Clicking in the overlapped area will cause the window to disappear.

1 Answer
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This problem is caused by the opacity: .5 which is applied to the entire comment div through .downvoted-answer .comments. The flag window is also affected by its grandparents opacity and this messes with the z-layers.

The easy fix is to apply any opacity changes to the individual comment sections instead: